# Package picard.sam

package picard.sam

Related Packages
Package
Description
picard
picard.sam.markduplicates
picard.sam.SamErrorMetric
picard.sam.util
Class
Description
AbstractAlignmentMerger
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
AbstractAlignmentMerger.UnmappingReadStrategy
AddCommentsToBam
A tool to add comments to a BAM file header.
AddOATag
AddOrReplaceReadGroups
Assigns all the reads in a file to a single new read-group.
BamIndexStats
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
BestEndMapqPrimaryAlignmentStrategy
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
BestMapqPrimaryAlignmentSelectionStrategy
This strategy was designed for TopHat output, but could be of general utility.
BuildBamIndex
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
CalculateReadGroupChecksum
CheckTerminatorBlock
Simple class to check the terminator block of a SAM file.
CleanSam
CompareSAMs
Rudimentary SAM comparer.
CreateSequenceDictionary
Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
DownsampleSam
Summary
DuplicationMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
DuplicationMetricsFactory
Factory class that creates either regular or flow-based duplication metrics.
EarliestFragmentPrimaryAlignmentSelectionStrategy
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
FastqToSam
Converts a FASTQ file to an unaligned BAM or SAM file.
FilterSamReads
Summary
FilterSamReads.Filter
FixMateInformation
Summary
FlowBasedDuplicationMetrics
GatherBamFiles
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
MergeBamAlignment
Summary
MergeSamFiles
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
MostDistantPrimaryAlignmentSelectionStrategy
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
PositionBasedDownsampleSam
Summary
PrimaryAlignmentSelectionStrategy
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
ReorderSam
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReplaceSamHeader
RevertOriginalBaseQualitiesAndAddMateCigar
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Used as a return for the canSkipSAMFile function.
RevertSam
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
RevertSam.FileType
SamAlignmentMerger
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
SamComparisonMetric
Metric for results of SamComparison.
SamFormatConverter
Converts a BAM file to human-readable SAM output or vice versa
SamToFastq
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
SamToFastqWithTags
Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
SetNmAndUqTags
Deprecated.
SetNmMdAndUqTags
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
SortSam
Sorts a SAM or BAM file.
SplitSamByLibrary
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
SplitSamByNumberOfReads
Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
ValidateSamFile
This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
ValidateSamFile.Mode
ViewSam
Prints a SAM or BAM file to the screen.
ViewSam.AlignmentStatus
ViewSam.PfStatus